Contacts of the strand formed by residues 125 - 133 (chain A) in PDB entry 1GNG


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLU 125 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LEU*     3.7    33.8    -      -       +      +
     89A  GLN      3.3    12.6    -      -       -      +
     90A  ASP*     4.6     5.8    -      -       +      -
     91A  LYS*     4.0     6.4    +      -       -      +
    120A  GLY*     3.0    24.3    +      -       -      -
    121A  GLU      5.4     0.2    +      -       -      -
    122A  LYS*     2.7    59.3    +      -       +      +
    123A  LYS*     3.3     3.1    +      -       -      +
    124A  ASP*     1.3    86.5    -      -       -      +
    126A  VAL*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LEU*     3.5     4.5    -      -       -      +
     89A  GLN*     2.6    53.8    +      -       +      +
     91A  LYS*     3.5    43.3    -      -       +      +
    117A  TYR*     4.2    29.2    -      -       +      -
    118A  SER      3.8    13.9    -      -       -      +
    119A  SER*     5.6     0.7    -      -       -      -
    120A  GLY*     4.2     2.9    -      -       -      +
    125A  GLU*     1.3    73.0    -      -       -      +
    127A  TYR*     1.3    60.5    +      -       -      +
    128A  LEU      4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     3.6    38.6    -      -       +      -
     87A  VAL      3.0    18.6    -      -       -      +
     88A  LEU*     3.4    38.4    -      -       +      +
    117A  TYR*     3.4     5.0    -      -       -      -
    118A  SER*     2.9    35.7    +      -       -      -
    119A  SER      3.5    25.6    -      -       -      -
    120A  GLY*     3.9    12.6    -      -       -      -
    121A  GLU*     4.5    10.3    +      -       +      +
    126A  VAL*     1.3    73.4    -      -       -      +
    128A  LEU*     1.3    60.2    +      -       -      +
    129A  ASN*     3.2     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LYS      3.2     4.5    -      -       -      +
     86A  LYS*     3.3     2.8    -      -       -      -
     87A  VAL*     2.9    33.7    +      -       +      +
     89A  GLN*     4.9     7.3    -      -       +      +
     95A  ASN*     3.6    28.7    -      -       +      +
     98A  LEU*     3.4    37.0    -      -       +      -
    115A  PHE*     3.8    22.9    -      -       +      -
    116A  PHE      3.7     6.7    -      -       -      +
    117A  TYR*     3.7    32.9    -      -       +      +
    126A  VAL      4.0     2.0    +      -       -      -
    127A  TYR*     1.3    73.6    -      -       -      +
    129A  ASN*     1.3    68.1    +      -       -      +
    130A  LEU*     3.8    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  TYR*     5.8     0.2    -      -       -      -
     84A  ILE*     4.1     9.8    -      -       +      +
     85A  LYS      3.4     3.4    -      -       -      -
     86A  LYS*     3.3    29.6    -      -       -      +
    115A  PHE*     3.2    23.8    -      -       -      -
    116A  PHE*     2.7    52.3    +      -       +      +
    118A  SER*     3.0    27.1    +      -       -      -
    127A  TYR      3.2    20.8    +      -       -      -
    128A  LEU*     1.3    73.9    -      -       -      +
    130A  LEU*     1.3    64.2    +      -       -      +
    131A  VAL*     3.3     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ILE*     3.2     3.1    -      -       -      -
     85A  LYS*     2.9    55.7    +      -       +      +
     87A  VAL*     4.6     9.2    -      -       +      -
     95A  ASN*     5.6     0.9    -      -       -      +
     97A  GLU*     3.8    37.2    -      -       +      +
     98A  LEU*     4.4    19.5    -      -       +      +
    101A  MET*     4.7     9.6    -      -       +      -
    112A  LEU*     3.8    17.7    -      -       +      -
    114A  TYR      4.0     0.4    -      -       -      -
    115A  PHE*     4.4     1.8    -      -       -      -
    128A  LEU*     3.8    28.9    -      -       +      +
    129A  ASN*     1.3    70.9    -      -       -      +
    131A  VAL*     1.3    61.9    +      -       -      +
    132A  LEU*     3.4    16.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  VAL*     5.9     4.0    -      -       +      -
     56A  TYR*     6.4     0.4    -      -       +      -
     75A  LEU*     5.1     6.1    -      -       +      -
     82A  VAL*     3.7    30.5    -      -       +      -
     83A  ALA      3.4     3.1    -      -       -      +
     84A  ILE*     4.0    14.4    -      -       +      +
    112A  LEU*     3.7     1.3    -      -       -      +
    113A  ARG*     2.9    36.4    +      -       +      +
    114A  TYR*     2.9    33.5    +      -       +      +
    116A  PHE*     3.6    34.3    -      -       +      -
    129A  ASN      3.6     4.3    -      -       -      +
    130A  LEU*     1.3    69.0    -      -       -      +
    132A  LEU*     1.3    58.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  VAL*     2.9    28.1    -      -       -      +
     83A  ALA*     2.7    23.0    +      -       +      +
     85A  LYS*     4.7    21.3    -      -       +      -
     97A  GLU*     5.5     4.9    -      -       -      +
    101A  MET*     4.2    23.1    -      -       +      -
    110A  VAL*     4.3    14.1    -      -       +      -
    111A  ARG      3.7     8.5    -      -       -      +
    112A  LEU*     3.8    22.9    -      -       +      -
    113A  ARG*     4.4     0.7    -      -       -      -
    130A  LEU*     4.0    19.1    -      -       +      +
    131A  VAL*     1.3    73.6    -      -       -      +
    133A  ASP*     1.3    68.0    +      -       -      +
    199A  CYS*     6.2     0.9    -      -       +      -
    200A  ASP*     5.7     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLU*     4.3     2.4    -      -       -      +
     81A  LEU      4.6     1.7    -      -       -      +
     82A  VAL*     4.3     4.8    -      -       -      +
     83A  ALA*     4.2     5.3    -      -       -      +
    110A  VAL*     3.5    24.6    -      -       +      +
    111A  ARG*     2.8    55.0    +      -       -      +
    113A  ARG*     3.4    28.6    +      -       -      +
    132A  LEU*     1.3    79.0    -      -       -      +
    134A  TYR*     1.3    62.6    +      -       -      +
    135A  VAL*     4.0     7.0    +      -       +      -
    188A  LEU*     4.5     5.4    -      -       -      +
    197A  LYS*     5.7     8.5    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il